Yes, on paid plans. Each store location has its own stock levels, and you can transfer stock between them with a full record of the movement.
A waybill is a delivery note generated straight from an invoice, with the same items but no prices shown, meant for your dispatch or delivery staff. Open any invoice and generate one in a click.
A receipt is issued automatically each time a payment is recorded, not when the invoice is created. An invoice with no payment yet has no receipt; that's expected, since a receipt proves money was received, not that a sale happened.
Yes, negotiated pricing on a customer's page lets you override the standard selling price for that customer only, applied automatically on new invoices.